PDB
5L7I
Resolution
3.3 Å
Released
July 20, 2016
Receptor
SMO
Class
F
Species
Homo sapiens
Ligand
Function
vismodegib
Antagonist
Reference
10.1038/NATURE18934

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Ligand Amino Acid Generic Number Segment Interaction Type
vismodegib N219 N-term Van der Waals
vismodegib L221 N-term hydrophobic
vismodegib M230 1.32x32 TM1 Van der Waals
vismodegib W281 2.58x58 TM2 hydrophobic
vismodegib W281 2.58x58 TM2 aromatic (edge-to-face)
vismodegib D384 ECL2 Van der Waals
vismodegib V386 ECL2 hydrophobic
vismodegib S387 ECL2 Van der Waals
vismodegib I389 ECL2 Van der Waals
vismodegib F391 45.51x51 ECL2 aromatic (edge-to-face)
vismodegib Y394 ECL2 polar (hydrogen bond)
vismodegib Y394 ECL2 hydrophobic
vismodegib R400 5.43x44 TM5 aromatic (pi-cation)
vismodegib H470 6.51x51 TM6 Van der Waals
vismodegib D473 6.54x54 TM6 hydrophobic
vismodegib Q477 6.58x58 TM6 Van der Waals
vismodegib W480 6.61x61 TM6 hydrophobic
vismodegib F484 6.65x65 TM6 Van der Waals
vismodegib P513 ECL3 hydrophobic
vismodegib E518 7.38x38 TM7 Van der Waals
vismodegib N521 7.41x41 TM7 Van der Waals
vismodegib L522 7.42x42 TM7 hydrophobic
vismodegib M525 7.45x45 TM7 hydrophobic

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Snake plot — Download: PNG | SVG
ICL1 W R N S N ICL1ECL1 M D G A R R E I V C R A D G T M R L G E P T S N E T ECL1ICL2 L G T T Y Q P L S G ICL2ECL2 Q V D G D S V S G I C F V G Y K ECL2ICL3 P G L L ICL3ECL3 G L P T K Q P I P D C E I K N R P ECL3N-term M A A A R P A R G P E L P L L G L L L L L L L G D P G R G A A S S G N A T G P G P R S A G G S A R R S A A V T G P P P P L S H C G R A A P C E P L R Y N V C L G S V L P Y G A T S T L L A G D S D S Q E E A H G K L V L W S G L R N A P R C W A V I Q P L L C A V Y M P K C E N D R V E L P S R T L C Q A T R G P C A I V E R E R G W P D F L R C T P D R F P E G C T N E V Q N I K F N S S G Q C E V P L V R T D N P K S W Y E D V E G C G I Q C Q N P L F N-termC-term G Q S D D E P K R I K K S K M I A K A F S K R H E L L Q N P G Q E L S F S M H T V S H D G P V A G L A F D L N E P S A D V S S A W A Q H V T K M V A R R G A I L P Q D I S V T P V A T P V P P E E Q A N L W L V E A E I S P E L Q K R L G R K K K R R K R K K E V C P L A P P P E L H P P A P A P S T I P R L P Q L P R Q K C L V A A G A W G A G D S C R Q G A W T L V S N P F C P E P S P P Q D P F L P S A P A P V A W A H G R R Q G L G P I H S R T N L M D T E L M D A D S D F C-term T E A E H Q D M H S Y I A A F G A V T G L C T L F T L A T F V A D R Y P A V I L F Y V N A C F F V G S I G W L A Q F L S C V I I F V I V Y Y A L M A G V V W F V V L T Y A W H T S F K A K T S Y F H L L T W S L P F V L T V A I L A V A N Y R Y R A G F V L A P I G L V L I V G G Y F L I R G V M T L F S I K S N H S E K A A S K I N E T M L R L G I F G F L A F G F V L I T F S C H F Y D F F N Q A E W E R S F R D Y V L C Q A N V T I S L L V E K I N L F A M F G T G I A M S T W V W T K A W R R L T T L L I T W C R
Helix box plot — Download: PNG | SVG L T C L G T V A G F A A I Y S H M D Q H 1 F Y V N A C F F V G S I G W L A Q F 2 V V F W V V G A M L A Y Y V I V F I I V 3 T S Y F H L L T W S L P F V L T V A I L 4 L F Y G G V I L V L G I P A L V F G A R Y 5 G I F G F L A F G F V L I T F S C H F Y 6 T S M A I G T G F M A F L N I K E V L L 7

GPCRdb(A)
GPCRdb(F)
SMO
TM1
1x35 1.32x32 M230
TM2
2x57 2.58x58 W281
ECL2
45x51 45.51x51 F391
TM5
5x40 5.43x44 R400
TM6
6x55 6.51x51 H470
6x58 6.54x54 D473
6x62 6.58x58 Q477
6x65 6.61x61 W480
6x69 6.65x65 F484
TM7
7x35 7.38x38 E518
7x38 7.41x41 N521
7x39 7.42x42 L522
7x42 7.45x45 M525